Scientific Publications

Citing Ensembl

If you would like to include a general reference to the Ensembl system in your work, we recommend citing the most recent overview article. For more specialised aspects of our system, further articles are listed below.

Citing Ensembl Data

Since release 25, all Ensembl releases have been archived as fully functional sites for about two years. This makes it possible to accurately cite data being referred to in a paper, even though the main Ensembl site is being continuously updated (currently release 54 - May 2009). For more information see the list of current archives.

Publications

T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, G. Coates, S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon, S. Gräf, S. Haider, M. Hammond, R. Holland, K. Howe, A. Jenkinson, N. Johnson, A. Kähäri, D. Keefe, S. Keenan, R. Kinsella, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios, M. Schuster, G. Slater, D. Smedley, W. Spooner, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, S. Wilder, A. Zadissa, E. Birney, F. Cunningham, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, A. Kasprzyk, G. Proctor, J. Smith, S. Searle, and P. Flicek
Ensembl 2009
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: D690-D697;
doi:10.1093/nar/gkn828
[Abstract] [Full text]
A.J. Vilella, J. Severin, A. Ureta-Vidal, R. Durbin, L. Heng, and E. Birney
EnsemblCompara GeneTrees: Analysis of complete, duplication-aware phylogenetic trees in vertebrates.
Genome Research 2009, 19:327-335
doi:10.1101/gr.073585.107
P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, T. Eyre, S. Fitzgerald, J. Fernandez-Banet, S. Gräf, S. Haider, M. Hammond, R. Holland, K. L. Howe, K. Howe, N. Johnson, A. Jenkinson, A. Kähäri, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. J. Vilella, J. Vogel, S. White, M. Wood, E. Birney, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, T. J. P. Hubbard, A. Kasprzyk, G. Proctor, J. Smith, A. Ureta-Vidal, and S. Searle.
Ensembl 2008
Nucleic Acids Res. 2008 Jan;36 Database issue:D707-14.
doi:10.1093/nar/gkm988
[Abstract] [Full text]
B. Paten, J. Herrero, S. Fitzgerald, K. Beal, P. Flicek, I. Holmes, and E. Birney
Genome-wide nucleotide-level mammalian ancestor reconstruction
Genome Research 2008 18: 1829-1843
doi:10.1101/gr.076521.108
B. Paten, J. Herrero, K. Beal, S. Fitzgerald, and E. Birney
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
Genome Research 2008 18: 1814-1828
doi:10.1101/gr.076554.108
Giulietta Spudich, Xosé M. Fernández-Suárez, and Ewan Birney
Genome Browsing with Ensembl: a practical overview
Brief Funct Genomic Proteomic, 2007 Sept; 6: 202-219
Xosé M. Fernández-Suárez and Michael K. Schuster
Using the Ensembl Genome Server to Browse Genomic Sequence Data.
UNIT 1.15 in Current Protocols in Bioinformatics, Supplement 16, January 2007.
T. J. P. Hubbard, B. L. Aken, K. Beal1, B. Ballester1, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, S. Graf, S. Haider, M. Hammond, J. Herrero, R. Holland, K. Howe, K. Howe, N. Johnson, A. Kahari, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, C. Melsopp, K. Megy, P. Meidl, B. Overduin, A. Parker, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, M. Wood, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, A. Kasprzyk, G. Proctor, S. Searle, J. Smith, A. Ureta-Vidal and E. Birney
Ensembl 2007
Nucleic Acids Res. 2007 Vol. 35, Database issue:D610-D617.
doi:10.1093/nar/gkl996
[Abstract] [Full text]
E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, S. Gräf, M. Hammond, J. Herrero, K. Howe, V. Iyer, K. Jekosch, A. Kähäri, A. Kasprzyk, D. Keefe, F. Kokocinski, E. Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A. Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster, I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A. Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and T. J. P. Hubbard
Ensembl 2006
Nucleic Acids Res. 2006 Jan 1;34 Database issue:D556-D561.
doi:10.1093/nar/gkj133
[Abstract] [Full text]
Guy St. C. Slater and Ewan Birney
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics. 2005 Feb 15;6(1):31
doi:10.1186/1471-2105-6-31
T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark and E. Birney
Ensembl 2005
Nucleic Acids Res. 2005 Jan 1;33 Database issue:D447-D453.
doi:10.1093/nar/gki138
[Abstract] [Full text]
J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, L. Wilming and T. Hubbard
The Vertebrate Genome Annotation (Vega) database.
Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D459-D465.
doi:10.1093/nar/gki135
[Abstract] [Full text]
International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature. 2004 Dec 9;432(7018):695-716.
doi:10.1038/nature03154
International Human Genome Sequencing Consortium.
Finishing the euchromatic sequence of the human genome
Nature. 2004 Oct 21;431(7011):931-945.
doi:10.1038/nature03001
Martin P. Hammond and Ewan Birney
Genome information resources - developments at Ensembl
Trends Genet. 2004 Jun; 20(6):268-272.
doi:10.1016/j.tig.2004.04.002
Genome Research Ensembl Special
The May 2004 issue of Genome Research includes an Ensembl special covering detailed aspects of the Ensembl web site, the underlying scalable database system for storing genome sequence and annotation information, as well as the automated genome analysis and annotation pipeline.
- Ewan Birney, T. Daniel Andrews, Paul Bevan, Mario Caccamo, Yuan Chen, Laura Clarke, Guy Coates, James Cuff, Val Curwen, Tim Cutts, Thomas Down, Eduardo Eyras, Xose M. Fernandez-Suarez, Paul Gane, Brian Gibbins, James Gilbert, Martin Hammond, Hans-Rudolf Hotz, Vivek Iyer, Kerstin Jekosch, Andreas Kahari, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehvaslaiho, Graham McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon Potter, Glenn Proctor, Mark Rae, Steve Searle, Guy Slater, Damian Smedley, James Smith, Will Spooner, Arne Stabenau, James Stalker, Roy Storey, Abel Ureta-Vidal, K. Cara Woodwark, Graham Cameron, Richard Durbin, Anthony Cox, Tim Hubbard, and Michele Clamp
  An Overview of Ensembl
  Genome Res. 2004 May; 14(5):925-928.
  [Abstract] [Full text]
- Arne Stabenau, Graham McVicker, Craig Melsopp, Glenn Proctor, Michele Clamp, and Ewan Birney
  The Ensembl Core Software Libraries
  Genome Res. 2004 May; 14(5):929-933.
  [Abstract] [Full text]
- Simon C. Potter, Laura Clarke, Val Curwen, Stephen Keenan, Emmanuel Mongin, Stephen M.J. Searle, Arne Stabenau, Roy Storey, and Michele Clamp
  The Ensembl Analysis Pipeline
  Genome Res. 2004 May; 14(5):934-941.
  [Abstract] [Full text]
- Val Curwen, Eduardo Eyras, T. Daniel Andrews, Laura Clarke, Emmanuel Mongin, Steven M.J. Searle, and Michele Clamp
  The Ensembl Automatic Gene Annotation System
  Genome Res. 2004 May; 14(5):942-950.
  [Abstract] [Full text]
- James Stalker, Brian Gibbins, Patrick Meidl, James Smith, William Spooner, Hans-Rudolf Hotz, and Antony V. Cox
  The Ensembl Web Site: Mechanics of a Genome Browser
  Genome Res. 2004 May; 14(5):951-955.
  [Abstract] [Full text]
- Stephen B. Montgomery, Tamara Astakhova, Mikhail Bilenky, Ewan Birney, Tony Fu, Maik Hassel, Craig Melsopp, Marcin Rak, A. Gordon Robertson, Monica Sleumer, Asim S. Siddiqui, and Steven J.M. Jones
  Sockeye: A 3D Environment for Comparative Genomics
  Genome Res. 2004 May; 14(5):956-962.
  [Abstract] [Full text]
- Stephen M.J. Searle, James Gilbert, Vivek Iyer, and Michele Clamp
  The Otter Annotation System
  Genome Res. 2004 May; 14(5):963-970.
  [Abstract] [Full text]
- James A. Cuff, Guy M.P. Coates, Tim J.R. Cutts, and Mark Rae
  The Ensembl Computing Architecture
  Genome Res. 2004 May; 14(5):971-975.
  [Abstract] [Full text]
- Eduardo Eyras, Mario Caccamo, Val Curwen, and Michele Clamp
  ESTGenes: Alternative Splicing From ESTs in Ensembl
  Genome Res. 2004 May; 14(5):976-987.
  [Abstract] [Full text]
- Ewan Birney, Michele Clamp, and Richard Durbin GeneWise and Genomewise
  Genome Res. 2004 May; 14(5):988-995.
  [Abstract] [Full text]
Rat Genome Sequencing Project Consortium.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature. 2004 Apr 1;428(6982):493-521.
doi:10.1038/nature02426
Emmanuel Mongin, Christos Louis, Robert A. Holt, Ewan Birney and Frank H. Collins
The Anopheles gambiae genome: an update.
Trends Parasitol. 2004 Feb; 20(2):49-52.
doi:10.1016/j.pt.2003.11.003
Arek Kasprzyk, Damian Keefe, Damian Smedley, Darin London, William Spooner, Craig Melsopp, Martin Hammond, Philippe Rocca-Serra, Tony Cox and Ewan Birney
EnsMart: A Generic System for Fast and Flexible Access to Biological Data.
Genome Res. 2004 Jan; 14(1):160-169.
[Full text]
E. Birney, D. Andrews, P. Bevan, M. Caccamo, G. Cameron, Y. Chen, L. Clarke, G. Coates, T. Cox, J. Cuff, V. Curwen, T. Cutts, T. Down, R. Durbin, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H. Hotz, V. Iyer, A. Kahari, K. Jekosch, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, C. Woodwark, M. Clamp and T. Hubbard
Ensembl 2004
Nucleic Acids Res. 2004 Jan 1;32 Database issue:D468-70.
[Abstract] [Full text]
M. Clamp, D. Andrews, D. Barker, P. Bevan, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, T. Hubbard, A. Kasprzyk, D. Keefe, H. Lehvaslaiho, V. Iyer, C. Melsopp, E. Mongin, R. Pettett, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik and E. Birney
Ensembl 2002: accommodating comparative genomics.
Nucleic Acids Res. 2003 Jan 1;31(1):38-42.
[Abstract] [Full text]
Mouse Genome Sequencing Consortium.
Initial sequencing and comparative analysis of the mouse genome.
Nature. 2002 Dec 5;420(6915):520-562.
doi:10.1038/nature01262
T. Hubbard, D. Barker, E. Birney, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik and M. Clamp.
The Ensembl genome database project.
Nucleic Acids Res. 2002 Jan 1; 30(1):38-41.
[Abstract] [Full text]